Dear Amber Users
I prepared the protein ligand system prmtop and inpcrd files following the
antechamber tutorial these command I use
source leaprc.protein.ff14SB
source leaprc.gaff
source leaprc.water.tip3p
loadamberparams 1DX.frcmod
loadoff 1dx.lib
complex = loadpdb hbay.pdb
solvatebox complex TIP3PBOX 10.0
addions complex Na+ 0
addions complex Cl- 0
saveamberparam hbay.prmtop hbay.inpcrd
leap log show after saveamberparam
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
** Warning: No sp2 improper torsion term for C*-CN-CB-CA
atoms are: CG CE2 CD2 CE3
** Warning: No sp2 improper torsion term for NA-CA-CN-CB
atoms are: NE1 CZ2 CE2 CD2
total 628 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
(Residues lacking connect0/connect1 -
these don't have chain types marked:
res total affected
1DX 1
CSER 1
NMET 1
WAT 9055
)
(no restraints)
> savepdb complex hbay_1DX.pdb
Writing pdb file: hbay_1DX.pdb
printing CRYST1 record to PDB file with box info
Converting N-terminal residue name to PDB format: NMET -> MET
Converting C-terminal residue name to PDB format: CSER -> SER
> quit
I also attaching leap log file kindly guide
After that I ran the simulation by using sander it ran but when i tried it
to run on the cluster by using pmemd it gives error message
Unit 9 Error on OPEN: hbay.inpcrd
PMEMD TERMINATED ABNORMALLY
Kind Regards
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Received on Fri Sep 22 2017 - 08:30:03 PDT
